Molecular analysis of chordomas and identification of therapeutic targets

Chordoma is a rare malignant bone tumour, showing notochordal differentiation, which occurs in the axial skeleton. Brachyury, a molecule involved in notochordal development, is a highly specific and sensitive marker for chordoma. It is hypothesised that brachyury or genes involved in its activation are implicated in the pathogenesis of chordoma. As there is currently no effective drug therapy for chordoma the aim of this study was to identify genetic events involved in chordoma pathogenesis with a view to identifying potential therapeutic targets. One hundred chordomas (50 skull-based, 50 non-skull based) were studied. Immunohistochemistry showed that the PI3K/AKT/TSC/mTOR pathway was activated in 65% of chordomas, thereby providing a rationale for testing mTOR inhibitors for the treatment of selected cases. DNA sequencing revealed no mutations in PI3KCA or RAS homologue enriched in brain (Rheb) in 23 tumours. Immunohistochemistry and Western blotting showed activation of the fibroblastic growth factor receptor (FGFR)/RAS/RAF/MEK/ERK/ETS2/brachyury pathway in more than 90% of cases, but no mutations were found in the genes analysed (FGFRs, KRAS, BRAF and brachyury) in 23 tumours. Three percent of cases revealed brachyury amplification but nearly half of the cases showed chromosomal abnormalities involving the brachyury locus. Knockdown of brachyury was achieved in the U-CH1 chordoma cell line using shRNA and resulted in premature cell senescence. These findings demonstrate that brachyury plays an important role in chordoma pathology. FISH analysis showed EGFR copy number gain in 45% of chordomas, including 6% with amplification and 39% with high level polysomy. The EGFR inhibitor, tyrphostin (AG1478) significantly inhibited growth of the chordoma cell line, and Western blotting showed this was associated with reduced phosphorylation of EGFR in a dose dependent manner. This study provides evidence for the first time that selected chordomas may be susceptible to treatment with EGFR inhibitors

Genome-wide association and Mendelian randomisation analysis provide insights into the pathogenesis of heart failure

Heart failure (HF) is a leading cause of morbidity and mortality worldwide. A small proportion of HF cases are attributable to monogenic cardiomyopathies and existing genome-wide association studies (GWAS) have yielded only limited insights, leaving the observed heritability of HF largely unexplained. We report results from a GWAS meta-analysis of HF comprising 47,309 cases and 930,014 controls. Twelve independent variants at 11 genomic loci are associated with HF, all of which demonstrate one or more associations with coronary artery disease (CAD), atrial fibrillation, or reduced left ventricular function, suggesting shared genetic aetiology. Functional analysis of non-CAD-associated loci implicate genes involved in cardiac development (MYOZ1, SYNPO2L), protein homoeostasis (BAG3), and cellular senescence (CDKN1A). Mendelian randomisation analysis supports causal roles for several HF risk factors, and demonstrates CAD-independent effects for atrial fibrillation, body mass index, and hypertension. These findings extend our knowledge of the pathways underlying HF and may inform new therapeutic strategies

The evolving SARS-CoV-2 epidemic in Africa: Insights from rapidly expanding genomic surveillance

INTRODUCTION Investment in Africa over the past year with regard to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sequencing has led to a massive increase in the number of sequences, which, to date, exceeds 100,000 sequences generated to track the pandemic on the continent. These sequences have profoundly affected how public health officials in Africa have navigated the COVID-19 pandemic. RATIONALE We demonstrate how the first 100,000 SARS-CoV-2 sequences from Africa have helped monitor the epidemic on the continent, how genomic surveillance expanded over the course of the pandemic, and how we adapted our sequencing methods to deal with an evolving virus. Finally, we also examine how viral lineages have spread across the continent in a phylogeographic framework to gain insights into the underlying temporal and spatial transmission dynamics for several variants of concern (VOCs). RESULTS Our results indicate that the number of countries in Africa that can sequence the virus within their own borders is growing and that this is coupled with a shorter turnaround time from the time of sampling to sequence submission. Ongoing evolution necessitated the continual updating of primer sets, and, as a result, eight primer sets were designed in tandem with viral evolution and used to ensure effective sequencing of the virus. The pandemic unfolded through multiple waves of infection that were each driven by distinct genetic lineages, with B.1-like ancestral strains associated with the first pandemic wave of infections in 2020. Successive waves on the continent were fueled by different VOCs, with Alpha and Beta cocirculating in distinct spatial patterns during the second wave and Delta and Omicron affecting the whole continent during the third and fourth waves, respectively. Phylogeographic reconstruction points toward distinct differences in viral importation and exportation patterns associated with the Alpha, Beta, Delta, and Omicron variants and subvariants, when considering both Africa versus the rest of the world and viral dissemination within the continent. Our epidemiological and phylogenetic inferences therefore underscore the heterogeneous nature of the pandemic on the continent and highlight key insights and challenges, for instance, recognizing the limitations of low testing proportions. We also highlight the early warning capacity that genomic surveillance in Africa has had for the rest of the world with the detection of new lineages and variants, the most recent being the characterization of various Omicron subvariants. CONCLUSION Sustained investment for diagnostics and genomic surveillance in Africa is needed as the virus continues to evolve. This is important not only to help combat SARS-CoV-2 on the continent but also because it can be used as a platform to help address the many emerging and reemerging infectious disease threats in Africa. In particular, capacity building for local sequencing within countries or within the continent should be prioritized because this is generally associated with shorter turnaround times, providing the most benefit to local public health authorities tasked with pandemic response and mitigation and allowing for the fastest reaction to localized outbreaks. These investments are crucial for pandemic preparedness and response and will serve the health of the continent well into the 21st century

Reducing the environmental impact of surgery on a global scale: systematic review and co-prioritization with healthcare workers in 132 countries

Background Healthcare cannot achieve net-zero carbon without addressing operating theatres. The aim of this study was to prioritize feasible interventions to reduce the environmental impact of operating theatres. Methods This study adopted a four-phase Delphi consensus co-prioritization methodology. In phase 1, a systematic review of published interventions and global consultation of perioperative healthcare professionals were used to longlist interventions. In phase 2, iterative thematic analysis consolidated comparable interventions into a shortlist. In phase 3, the shortlist was co-prioritized based on patient and clinician views on acceptability, feasibility, and safety. In phase 4, ranked lists of interventions were presented by their relevance to high-income countries and low–middle-income countries. Results In phase 1, 43 interventions were identified, which had low uptake in practice according to 3042 professionals globally. In phase 2, a shortlist of 15 intervention domains was generated. In phase 3, interventions were deemed acceptable for more than 90 per cent of patients except for reducing general anaesthesia (84 per cent) and re-sterilization of ‘single-use’ consumables (86 per cent). In phase 4, the top three shortlisted interventions for high-income countries were: introducing recycling; reducing use of anaesthetic gases; and appropriate clinical waste processing. In phase 4, the top three shortlisted interventions for low–middle-income countries were: introducing reusable surgical devices; reducing use of consumables; and reducing the use of general anaesthesia. Conclusion This is a step toward environmentally sustainable operating environments with actionable interventions applicable to both high– and low–middle–income countries

Molecular analysis of chordomas and identification of therapeutic targets.

Chordoma is a rare malignant bone tumour, showing notochordal differentiation, which occurs in the axial skeleton. Brachyury, a molecule involved in notochordal development, is a highly specific and sensitive marker for chordoma. It is hypothesised that brachyury or genes involved in its activation are implicated in the pathogenesis of chordoma. As there is currently no effective drug therapy for chordoma the aim of this study was to identify genetic events involved in chordoma pathogenesis with a view to identifying potential therapeutic targets. One hundred chordomas (50 skull-based, 50 non-skull based) were studied. Immunohistochemistry showed that the PI3K/AKT/TSC/mTOR pathway was activated in 65% of chordomas, thereby providing a rationale for testing mTOR inhibitors for the treatment of selected cases. DNA sequencing revealed no mutations in PI3KCA or RAS homologue enriched in brain (Rheb) in 23 tumours. Immunohistochemistry and Western blotting showed activation of the fibroblastic growth factor receptor (FGFR)/RAS/RAF/MEK/ERK/ETS2/brachyury pathway in more than 90% of cases, but no mutations were found in the genes analysed (FGFRs, KRAS, BRAF and brachyury) in 23 tumours. Three percent of cases revealed brachyury amplification but nearly half of the cases showed chromosomal abnormalities involving the brachyury locus. Knockdown of brachyury was achieved in the U-CH1 chordoma cell line using shRNA and resulted in premature cell senescence. These findings demonstrate that brachyury plays an important role in chordoma pathology. FISH analysis showed EGFR copy number gain in 45% of chordomas, including 6% with amplification and 39% with high level polysomy. The EGFR inhibitor, tyrphostin (AG1478) significantly inhibited growth of the chordoma cell line, and Western blotting showed this was associated with reduced phosphorylation of EGFR in a dose dependent manner. This study provides evidence for the first time that selected chordomas may be susceptible to treatment with EGFR inhibitors.

Physical Properties of Sandy Soil Affected by Soil Conditioner Under Wetting and Drying cycles

Information on the effectiveness of soil conditioners over a prolonged period is scarce. A laboratory experiment was undertaken to evaluate the effectiveness of a polyacrylamide (Broadleaf P4) soil conditioner on the physical properties of sandy soil subjected to wetting and drying cycles. Four concentrations of Broadleaf P4 0, 0.2, 0.4, and 0.6% on dry weight basis were uniformly mixed with a calcareous sandy soil. Addition of Broadleaf P4 to sandy soil increased the water holding capacity, decreased the bulk density, and increased the porosity and void ratio at 0 and 16 wetting and drying cycles. The coefficient of linear extensibility increased considerably with increasing concentrations of the polymer. The addition of polymer at 0 and 16 cycles increased considerably the retention and availability of water in sandy soil. Saturated hydraulic conductivity decreased with increasing concentrations of Broadleaf P4 whereas unsaturated hydraulic conductivity at 0 and 16 cycles showed an increase with increasing soil moisture contents. After I6 wetting and drying cycles, the capacity of the soil to hold water was lost on average by 15.8% when compared to the 0 wetting and drying cycle. The effectiveness of the soil conditioner on bulk density, coefficient of linear extensibility, available water and saturated hydraulic conductivity was reduced on average by 14.1, 24.5, 21.l and 53.7% respectively. The significant changes in soil properties between 0 and 16 cycles suggested that the effectiveness of the conditioner decreased with the application of wetting and drying cycles. However, its effect was still considerable when compared to untreated soil under laboratory conditions

Physical Properties of Sandy Soil Affected by Soil Conditioner Under Wetting and Drying cycles

Information on the effectiveness of soil conditioners over a prolonged period is scarce. A laboratory experiment was undertaken to evaluate the effectiveness of a polyacrylamide (Broadleaf P4) soil conditioner on the physical properties of sandy soil subjected to wetting and drying cycles. Four concentrations of Broadleaf P4 0, 0.2, 0.4, and 0.6% on dry weight basis were uniformly mixed with a calcareous sandy soil. Addition of Broadleaf P4 to sandy soil increased the water holding capacity, decreased the bulk density, and increased the porosity and void ratio at 0 and 16 wetting and drying cycles. The coefficient of linear extensibility increased considerably with increasing concentrations of the polymer. The addition of polymer at 0 and 16 cycles increased considerably the retention and availability of water in sandy soil. Saturated hydraulic conductivity decreased with increasing concentrations of Broadleaf P4 whereas unsaturated hydraulic conductivity at 0 and 16 cycles showed an increase with increasing soil moisture contents. After I6 wetting and drying cycles, the capacity of the soil to hold water was lost on average by 15.8% when compared to the 0 wetting and drying cycle. The effectiveness of the soil conditioner on bulk density, coefficient of linear extensibility, available water and saturated hydraulic conductivity was reduced on average by 14.1, 24.5, 21.l and 53.7% respectively. The significant changes in soil properties between 0 and 16 cycles suggested that the effectiveness of the conditioner decreased with the application of wetting and drying cycles. However, its effect was still considerable when compared to untreated soil under laboratory conditions

Impact of Sewage Sludge on Water Movement in Calcareous Sandy Soils

The present study was undertaken to investigate the changes in soil physical properties and their effect on water movement under ponded irrigation. Sewage sludge was applied to 10 cm soil depth at rates of 0.25. 75  and 100 Mg-ha-1 to two disturbed soils differing in CaCO3 content. The results showed that cumulative infiltration (1) decreased with an increase in sewage sludge rates. Basic infiltration for slightly calcareous sandy soil was higher than that of moderately calcareous sandy soil, laboratory measurements showed an exponential decrease in saturated hydraulic conductivity and an increase in available water capacity with an increase in sewage sludge rates. For both soils, water diffusivity (D(Q)) decreased with an increase in sewage sludge rates. The (oral) values of slightly calcareous sandy soils were higher than those of moderately calcareous sandy soils

Impact of Sewage Sludge on Water Movement in Calcareous Sandy Soils

The present study was undertaken to investigate the changes in soil physical properties and their effect on water movement under ponded irrigation. Sewage sludge was applied to 10 cm soil depth at rates of 0.25. 75  and 100 Mg-ha-1 to two disturbed soils differing in CaCO3 content. The results showed that cumulative infiltration (1) decreased with an increase in sewage sludge rates. Basic infiltration for slightly calcareous sandy soil was higher than that of moderately calcareous sandy soil, laboratory measurements showed an exponential decrease in saturated hydraulic conductivity and an increase in available water capacity with an increase in sewage sludge rates. For both soils, water diffusivity (D(Q)) decreased with an increase in sewage sludge rates. The (oral) values of slightly calcareous sandy soils were higher than those of moderately calcareous sandy soils

The amplitude and phase distributions of cosmic ray variation at different conditions of Forbush decrease

The Forbush effect is one of the striking examples of irregular variations in the cosmic ray (CR) flux. It is a heliospheric phenomenon that includes a decrease and a recovery of the CR intensity and small changes in the CR density and anisotropy before the start of the main decrease. They were first noted as the effects of decreasing the intensity of cosmic rays, coinciding with geomagnetic storms. The increased interest is observed in recent years and it is primarily because their variables are strongly related to processes in solar-terrestrial physics. Forbush effects convey significant information regarding interplanetary disturbances. In the present work, fifty-three Forbush decrease (FD) events were categorized into four types according to their profile shape. From 1990 to 2020, cosmic ray intensity data from five neutron monitor stations (two subpolar and three mid-latitude) were used. The superposed epoch technique has been used to calculate the vectorial average of the observed diurnal vectors for every day of the four types of FD. It can be found that the subpolar stations (McMurdo and Thule) showed different behavior than the other stations. The solar-diurnal variation at the Thule and McMurdo subpolar stations is comparable on some days to the variation at mid-latitude stations, indicating that CR anisotropy on these days is not the only (and sometimes not the main) source of the solar-diurnal variation. The contribution of the solar-diurnal anisotropy to the diurnal variation at subpolar stations is small, much less than at other neutron monitors